The Changbai Mountains wild boar (Cetartiodactyla: Suidae) is an omnivorous, gregarious and non-hibernating animal that inhabits in Jilin province of China and is threatened by poaching and deforestation. In this study, we provide the first report of the complete mitogenome of Changbai Mountains wild boar. The total length of mitochondrial genome is 16,720 bp and consists of 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and a major non-coding control region (D-loop region). The D-loop region contains one repeat motif. The full complement of genes in the Changbai Mountains wild boar are located on the H-strand, except for the ND6 gene and eight tRNA genes that are encoded on the L-strand. Phylogenetic analysis based on combining 13 protein-coding gene sequences of several species showed that it is closely related to genus Sus scrofa in north China. The mitochondrial genome of Changbai Mountains wild boar is useful for population genetics and phylogenetic analysis.